PAPQMD parametrization of molecular systems with cyclopropyl rings: Conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid

The suitability of ab initio, semiempirical and density functional methods as sources of stretching and bending parameters has been explored using the PAPQMD (Program for Approximate Parametrization from Quantum Mechanical Data) strategy. Results show that semiempirical methods provide parameters comparable to those compiled on empirical force fields. In this respect the AM1 method seems to be a good method to obtain parameters at a minimum computational cost. On the other hand, harmonic force fields initially developed for proteins and DNA have been extended to include compounds containing highly strained three-membered rings, like 1-aminocyclopropane-1-carboxylic acid. For this purpose the cyclopropyl ring has been explicitly parametrized at the AM1 level considering different chemical environments. Finally, the new set of parameters has been used to investigate the conformational preferences of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid. Results indicate that such compounds tend to adopt a helical conformation stabilized by intramolecular hydrogen bonds between residues i and i+3. This conformation allows the arrangement of the cyclic side chains without steric clashes.     

A new strategy for the evaluation of force parameters from quantum mechanical computations

A new strategy for the determination of force parameters is presented. The equilibrium values appearing in the force field equations representing the “stretching” and “bending” of bonds are directly determined from quantum mechanical calculations without geometrical restrictions. The determination of the force parameters is carried out by means of a rigorous fitting between the quantum mechanic and the molecular mechanical energy variations arising from the perturbation of the geometric variables. The strategy presented here has been incorporated into a computer program named PAPQMD, which was developed in order to provide nonquantum mechanical experts with a powerful tool for the determination of approximate force parameters. The program was developed upon the assumption that force parameters are not universal, but they strongly depend on the molecular environment. This implies that the parametrization procedure should be done in a molecular model close to the molecule or molecules to be studied by means of molecular mechanical or dynamic methods, and consequently, it is no longer supposed that the variation of one geometrical parameter does not affect the rest of the molecular geometry. PAPQMD performs the fitting between molecular mechanics and quantum mechanical energies considering all the perturbations that the modification in one geometric variable causes in all the others, enabling the parametrization even of large molecules. The ability of our method to reproduce experimentally derived force parameters is discussed and compared with the widely used Hopfinger's strategy. The study of the behavior of PAPQMD and Hopfinger's strategies for reproducing the force parameters of two complex molecules demonstrates the superiority of the methodology presented here.     

Molecular properties from perturbation theory: A Unified treatment of energy derivatives

The definition of a molecular property as a derivative of the electronic energy with respect to one or more applied perturbations is reviewed. The explicit enumeration of terms entering the derivative formulas is performed by considering in turn the various parameter spaces on which the energy and wave function depend. After deriving general expressions for first, second, and third derivatives for different types of perturbation, the parameter spaces involved in MCSCF and CI cases are identified and used to obtain expressions for the first and second derivatives. An example of an MCSCF third derivative is also given. In addition, the various equation systems defining the perturbed wave functions in each order are derived. Some attention is given to the efficient computer implementation of derivative calculations, and the present work is compared with that of other authors.     

Structure of MCSCF electronic energy domain

The modern version of the process of removing redundant variables in an MCSCF optimization problem is studied on the basis of the manifold theory. It is shown that there exists a simple parametrization of the MCSCF orbital manifold that is convenient for computer implementation of quasi-Newton optimization schemes. A sequential unconstrained optimization technique for minimizing electronic energy with respect to local coordinates is described.     

A systematic ab initio study of the group V trihalides MX3 and pentahalides MX5 (M = P?Bi,X = F?I)

Ab initio calculations using effective core potentials and polarized split-valence basis sets are reported for the title compounds. The calculated geometries, vibrational frequencies, infrared intensities, harmonic force fields, dipole moments, relative energies, and barriers to pseudorotation are compared with the available experimental data for the known molecules. Predictions are made for those pentahalides that are still unknown. Trends in the calculated properties are identified and discussed.     

Partial hessian fitting for determining force constant parameters in molecular mechanics

We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond‐stretching, angle‐bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least‐squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER‐type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM‐calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal‐organic frameworks, the MM‐optimized geometry sometimes deviates significantly from the QM‐optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond‐stretching and angle‐bending terms. © 2016 Wiley Periodicals, Inc.     

Design and application of a multicoefficient correlation method for dispersion interactions

A new multicoefficient correlation method (MCCM) is presented for the determination of accurate van der Waals interactions. The method utilizes a novel parametrization strategy that simultaneously fits to very high-level binding, Hartree-Fock and correlation energies of homo- and heteronuclear rare gas dimers of He, Ne, and Ar. The decomposition of the energy into Hartree-Fock and correlation components leads to a more transferable model. The method is applied to the krypton dimer system, rare gas-water interactions, and three-body interactions of rare gas trimers He3, Ne3, and Ar3. For the latter, a very high-level method that corrects the rare-gas two-body interactions to the total binding energy is introduced. A comparison with high-level CCSD(T) calculations using large basis sets demonstrates the MCCM method is transferable to a variety of systems not considered in the parametrization. The method allows dispersion interactions of larger systems to be studied reliably at a fraction of the computational cost, and offers a new tool for applications to rare-gas clusters, and the development of dispersion parameters for molecular simulation force fields and new semiempirical quantum models.     

Multiconfiguration self-consistent-field theory based upon the fragment molecular orbital method

The fragment molecular orbital (FMO) method was combined with the multiconfiguration self-consistent-field (MCSCF) theory. One- and two-layer approaches were developed, the former involving all dimer MCSCF calculations and the latter limiting MCSCF calculations to a small part of the system. The accuracy of the two methods was tested using the six electrons in six orbitals complete active space type of MCSCF and singlet spin state for phenol+(H(2)O)(n), n=16,32,64 (6-31G( *) and 6-311G( *) basis sets); alpha helices and beta strands of phenylalanine-(alanine)(n), n=4,8,16 (6-31G( *)). Both double-zeta and triple-zeta quality basis sets with polarization were found to have very similar accuracy. The error in the correlation energy was at most 0.000 88 a.u., the error in the gradient of the correlation energy was at most 6.x10(-5) a.u./bohr and the error in the correlation correction to the dipole moment was at most 0.018 D. In addition, vertical singlet-triplet electron excitation energies were computed for phenol+(H(2)O)(n), (n=16,32,64), 6-31G( *), and the errors were found to be at most 0.02 eV. Approximately linear scaling was observed for the FMO-based MCSCF methods. As an example, an FMO-based MCSCF calculation with 1262 basis functions took 98 min on one 3.0 GHz Pentium4 node with 1 Gbyte RAM.     

Practical considerations for building GROMOS-compatible small-molecule topologies

Molecular dynamics simulations are being applied to increasingly complex systems, including those involving small endogenous compounds and drug molecules. In order to obtain meaningful and accurate data from these simulations, high-quality topologies for small molecules must be generated in a manner that is consistent with the derivation of the force field applied to the system. Often, force fields are designed for use with macromolecules such as proteins, making their transferability to other species challenging. Investigators are increasingly attracted to automated topology generation programs, although the quality of the resulting topologies remains unknown. Here we assess the applicability of the popular PRODRG server that generates small-molecule topologies for use with the GROMOS family of force fields. We find that PRODRG does not reproduce topologies for even the most well-characterized species in the force field due to inconsistent charges and charge groups. We assessed the effects of PRODRG-derived charges on several systems: pure liquids, amino acids at a hydrophobic-hydrophilic interface, and an enzyme-cofactor complex. We found that partial atomic charges generated by PRODRG are largely incompatible with GROMOS force fields, and the behavior of these systems deviates substantially from that of simulations using GROMOS parameters. We conclude by proposing several points as "best practices" for parametrization of small molecules under the GROMOS force fields.     

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development

This work presents a novel parametrization for the ReaxFF formalism as a means to investigate reaction processes of chlorinated organic compounds. Force field parameters cover the chemical elements C, H, O, Cl and were obtained using a novel optimization approach involving relaxed potential energy surface scans as training targets. The resulting ReaxFF parametrization shows good transferability, as demonstrated on two independent ab initio validation sets. While this first part of our two-paper series focuses on force field parametrization, we apply our parameters to the simulation of chlorinated dibenzofuran formation and decomposition processes in Part II.     

Basis set and correlation energy dependence of geometry and harmonic frequencies of difluoroethane,CHF2CH3

Optimum geometries and harmonic frequencies calculated at the Hartree–Fock and the MP2 level are reported for the fluorohydrocarbon CHF₂CH₃; basis sets employed range from STO-3G to 6-311G**. The significantly shortened C? C distance of 1.50 Å is reproduced already with the simplest split-valence basis set; the C? F distance of 1.36 Å on the other hand needs MP2 correction at least at the double-ζ or 6-311G* level. Symmetry coordinates defined in terms of internal coordinates are in qualitative agreement with available experimental evidence. Even the best basis set yields frequencies that differ from experimental (anharmonic) values by up to 200 cm^?1 indicating the well-known necessity of including higher-order force constants if quantitative agreement with experiment is to be achieved.     

Bond stretching force constants and compressibilities of nitride,oxide, and sulfide coordination polyhedra in molecules and crystals

Molecular quadratic stretching force constants are calculated for a variety of MX bonds (X = N, O, S) in coordinated polyhedra containing row 1 and 2 metal atoms, M, using SCF molecular orbital methods and 6-31G^* basis sets. The resulting data scatter along three distinct trends, depending on whether the bonds involve row 1 atoms, row 1 and row 2 atoms, or row 2 atoms. When compared with spectroscopically determined force constants, the calculated force constants are found to be 20% larger. A single trend seems to obtain when the calculated force constants are plotted as a function of the effective nuclear charges of the bonded atoms and their interatomic separations. Scaled force constants calculated for the SiO bond are in rough agreement with values provided by spectroscopic measurements for silicic acid molecules and silicate crystals. Polyhedral compressibilities for nitride-, oxide-, and sulfide-coordinated polyhedra are inversely related with force constants calculated for their MX bonds. The close similarity of these compressibilities and those recorded for chemically similar crystals suggests that force constant-compressibility relationships in chemically similar molecular and crystalline systems are not significantly different.     

An all-atom force field for metallocenes

A new all-atom force field, for the molecular modeling of metallocenes was constructed. Quantum chemical calculations were performed to obtain several force field terms not yet defined in the literature. The remainder were transferred from the OPLS-AA/AMBER framework. The parametrization work included the obtention of geometrical parameters, torsion energy profiles, and distributions of atomic charges that blend smoothly with the OPLS-AA specification for a variety of organic molecular fragments. Validation was carried out by comparing simulated and experimental data for five different ferrocene derivatives in the crystalline phase. The present model can be regarded as a step toward a general force field for metallocenes, built in a systematic way, easily integrated with OPLS-AA, and transferable between different metal-ligand combinations.     

Interpretation of the vibrational spectra of matrix-isolated uracil from scaled ab initio quantum mechanical force fields

The vibrational spectrum of uracil trapped in an argon matrix has been interpreted based on ab initio Hartree–Fock SCF calculations with a split-valence 4?21 basis set. The directly computed theoretical general valence force field was scaled with empirical scale factors in order to correct for the systematic errors originating in the limitation of the theoretical model. Scale factors transferred from related molecules provided a priori prediction of fundamental frequencies and intensities, permitting several corrections to be proposed for earlier assignments. Using the observed spectrum with the few altered assignments, a new set of scale factors was optimized to give the best force field available from combined consideration of the experimental and the theoretical data. For unknown reasons, the out-of-plane force field predicted a spectrum agreeing slightly less well with experiment than did the in-plane force field. However, the overall agreement between theory and experiment provided additional support for the assumptions involved in the method. The computed force fields were compared with others available from previous work. The comparison demonstrated the importance of expanding the energy surface around the true energy minimum and of using a proper scaling procedure. Previous scaled CNDO /2 calculations were found to be surprisingly good despite the large corrections required and the fact that they were made at an incorrect geometry.     

Rh2(CO)4(μ-Cl)2和Rh4(μ-CO)3(CO)4的简正振动分析

金属簇合物具有独特的结构和成键方式。本文对铑簇合物的简正振动分析进行了研究。通过红外光谱用石蜡油糊涂KBr和聚乙烯窗口, 在Nicolet 200SXV FT-IR光谱上测定了Rh2(CO)4(μ-Cl)2的构型, 并使用分子振动全分析程序MVTA(Basic语言), 在PC机上进行计算。     

FT-Raman and infrared spectra,r0 structural parameters,ab initio calculations and vibrational assignment for nitryl chloride

The FT-Raman spectra (2000-30 cm⁻¹) of liquid and solid nitryl chloride, ClNO₂, along with the infrared spectra (2000-80 cm⁻¹) of the gas and solid have been recorded. All six fundamentals are confidently identified and the potential energy distributions determined from the force fields obtained from ab initio calculations. Several different basis sets have been utilized to determine the harmonic frequencies and force constants which are compared to the previously reported valence force constants. Structural parameters have been calculated with these basis sets including electron correlation with MP2, MP3 and MP4 perturbation. The calculated equilibrium structural parameters are compared to the experimental r₀ structural parameters. The spectra of the solid indicate that there are at least two molecules per primitive cell. All of these results are compared to the corresponding quantities for some similar molecules.     

The propagation of basis-set error and geometry optimization in ab initio calculations. II. Correlation between the balance of Gaussian basis sets and calculated molecular properties

Basis-set balance parameters, defined in terms of various projections of an abstract force vector in the space spanned by the logarithms of orbital exponents, are evaluated for a sample of 100 Gaussian basis sets. These basis sets are taken from a random Gaussian distribution of bases, centered on the best energy, fully variational uniform quality (UQ) atomic orbital (AO) basis sets. With each basis geometry optimization has been carried out for model molecule dimethyl sulfoxide, the wavefunction of which molecule is exceptionally sensitive to basis-set errors. Correlations between the balance of basis sets and calculated molecular properties are analyzed.     

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field

Hydration free energy calculations are often used to validate molecular simulation methodologies and molecular mechanics force fields. We use the free-energy perturbation method together with the AMOEBA polarizable force field and the Poltype parametrization protocol to predict the hydration free energies of 52 molecules as part of the SAMPL4 blind challenge. For comparison, similar calculations are performed using the non-polarizable General Amber force field. Against our expectations, the latter force field gives the better results compared to experiment. One possible explanation is the sensitivity of the AMOEBA results to the conformation used for parametrization.